In June 2011, Ogmunder Jonasson, Iceland's minister of the interior at the time, received an urgent message from US authorities.

It said that "there was an imminent attack on Icelandic government databases" by hackers and that the FBI would send agents to investigate, Jonasson said in a telephone interview.

But when "eight or nine" FBI agents arrived in August, Jonasson said, he found that they were not investigating an imminent attack but gathering material on WikiLeaks, the activist group that has been responsible for publishing millions of confidential documents over the past three years and that has many operatives in Iceland.

Jonasson asked the agents to leave, he said, because they had misrepresented the purpose of their visit.

The operation in Iceland was part of a wide-ranging investigation into WikiLeaks and its founder, Julian Assange, for their roles in the release of US military and diplomatic documents in 2009 and 2010. The investigation has been quietly gathering material since at least October 2010, six months after the arrest of Private Bradley Manning, the US army enlistee who is accused of providing the bulk of the leaks.

Until he re-emerged last week as an ally for Edward Snowden, the former computer contractor who leaked details of National Security Agency surveillance, Assange looked like a forgotten man. WikiLeaks had not had a major release of information in several years, its funds had dwindled, and several senior architects of its systems left, citing internal disputes. Assange himself is holed up in the Ecuadorean embassy in London, where he fled to avoid extradition to Sweden for questioning on allegations of sexual abuse.

But the US government had not forgotten about him. Interviews with government agents, prosecutors and others familiar with the WikiLeaks investigation, as well as an examination of court documents, suggest that Assange and WikiLeaks are being investigated by at least four government agencies, along with a grand jury that has subpoenaed witnesses.

Tens of thousands of pages of evidence have been gathered. And at least four other former members of WikiLeaks have had contact with US authorities seeking information on Assange, the former members said, speaking on the condition of anonymity to discuss a matter they were informed was confidential.

In recent responses, a US Justice Department spokesman confirmed that it "has an investigation into matters involving WikiLeaks, and that investigation remains ongoing", but he declined to offer details.

The prosecution of WikiLeaks would put the administration into tricky legal territory. WikiLeaks is an international organisation and, unlike Manning and Snowden, Assange and the other members did not work for the US government or its contractors and could not be charged with espionage.

WikiLeaks maintains it was functioning as a publisher by enabling the release of information in the public interest, and it has frequently been a partner with traditional news organisations, including The New York Times and The Guardian. If the government charged WikiLeaks and Assange as co-conspirators, it would be arguing that, unlike their partners, they are not journalists.

"Given the government's aggression in the Snowden case, I would expect that the government will continue to move forward with the Assange case on a conspiracy theory, even though WikiLeaks would seem eligible for First Amendment protections," said James Goodale , a First Amendment lawyer and the author of Fighting for the Press. Assange says the Justice Department "and its accompanying FBI investigation are blinded by their zeal to get rid of publishers who speak truth to power".

The investigation has largely been carried out in secret, as most are, but a few clues have emerged. In December 2010, the US attorney for the Eastern District of Virginia requested Twitter account information for Manning, Assange and Birgitta Jonsdottir , a former WikiLeaks activist and now a member of Iceland's Parliament, among others.

A redacted version of the subpoena served on Jonsdottir cited a specific conspiracy provision that might have been aimed at those thought to have assisted Manning.

Other court orders have been disclosed. Last week, Herbert Snorrason, a former WikiLeaks member once close to Assange, wrote on his website that he had been provided orders, unsealed May 2, including a search warrant served on Google for "all e-mail associated with my Gmail account, every shred of information they had on my identity and anything I'd uploaded to a Google service."

Although no reason was given for the broad seizure of information, he said, he believes it is "because I had a conversation or a few with a white-haired Australian guy", a reference to Assange.

"These kinds of orders have been served on more of the people I know than I really care to think about," he said.

The pretrial hearings in the case of Manning have also provided some hints. According to testimony in Manning's hearings in 2011 and 2012, as transcribed by Alexa O'Brien , an activist who was present in court, Major Ashden Fein, on behalf of the prosecution, told the judge that an FBI file that contained information on Manning "is much broader" than just his case and contained secret grand jury testimony. He said the file contained 3,475 documents and ran to 42,135 pages.

The FBI's activities in Iceland provide perhaps the clearest view of the government's interest in Assange. A young online activist, Sigurdur Ingi Thordarson (known as Siggi), told a closed session of Iceland's Parliament this year that he had been co-operating with US agents investigating WikiLeaks at the time of the FBI's visit in 2011.

"He was at the time going back and forwards going to meet Julian" at Ellingham Hall, a rural English mansion where Assange was under house arrest and "they were trying to get him to go there wearing a wire," Jonsdottir said in an interview.

It was not clear to what extent he cooperated, Jonsdottir said. Some activists there believed he has been used as a double agent by Assange, gathering information about the investigation while he appeared to be co-operating.

Assange has alleged that there is a link between the allegations in Sweden and the US investigation, but no link has been shown.

"Julian is in an incredibly unfair situation where he has not been charged with a crime in any country, and the United States continues to place him in legal jeopardy by refusing to discuss the status of that investigation," said Jennifer Robinson, a member of his legal team in London, adding. "He is in a no-man's- land."

It is not clear how much longer the investigation might take. But a former official involved in the case said that any WikiLeaks investigation would probably run for "an exceptionally long time" before efforts were made to bring Assange to the United States.

The man who was at the centre of the most famous press leak of all, the Pentagon Papers, thinks Assange will eventually be charged.

"There are people who say he is being paranoid or unreasonable, but that does not mean that they are not out to get him," said Daniel Ellsberg, who was charged with releasing the Pentagon Papers, charges that were dismissed after there was evidence of illegal wiretapping by the government. "A grand jury has been convened, an investigation is under way, and I would be surprised if they did not go after him."